Literature DB >> 21984756

Visual DSD: a design and analysis tool for DNA strand displacement systems.

Matthew R Lakin1, Simon Youssef, Filippo Polo, Stephen Emmott, Andrew Phillips.   

Abstract

SUMMARY: The Visual DSD (DNA Strand Displacement) tool allows rapid prototyping and analysis of computational devices implemented using DNA strand displacement, in a convenient web-based graphical interface. It is an implementation of the DSD programming language and compiler described by Lakin et al. (2011) with additional features such as support for polymers of unbounded length. It also supports stochastic and deterministic simulation, construction of continuous-time Markov chains and various export formats which allow models to be analysed using third-party tools.

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Year:  2011        PMID： 21984756      PMCID： PMC3208393          DOI： 10.1093/bioinformatics/btr543

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  7 in total

1.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Authors:  M Hucka; A Finney; H M Sauro; H Bolouri; J C Doyle; H Kitano; A P Arkin; B J Bornstein; D Bray; A Cornish-Bowden; A A Cuellar; S Dronov; E D Gilles; M Ginkel; V Gor; I I Goryanin; W J Hedley; T C Hodgman; J-H Hofmeyr; P J Hunter; N S Juty; J L Kasberger; A Kremling; U Kummer; N Le Novère; L M Loew; D Lucio; P Mendes; E Minch; E D Mjolsness; Y Nakayama; M R Nelson; P F Nielsen; T Sakurada; J C Schaff; B E Shapiro; T S Shimizu; H D Spence; J Stelling; K Takahashi; M Tomita; J Wagner; J Wang
Journal:  Bioinformatics       Date:  2003-03-01       Impact factor: 6.937

2.  Enzyme-free nucleic acid logic circuits.

Authors:  Georg Seelig; David Soloveichik; David Yu Zhang; Erik Winfree
Journal:  Science       Date:  2006-12-08       Impact factor: 47.728

3.  A programming language for composable DNA circuits.

Authors:  Andrew Phillips; Luca Cardelli
Journal:  J R Soc Interface       Date:  2009-06-17       Impact factor: 4.118

4.  Scaling up digital circuit computation with DNA strand displacement cascades.

Authors:  Lulu Qian; Erik Winfree
Journal:  Science       Date:  2011-06-03       Impact factor: 47.728

5.  Neural network computation with DNA strand displacement cascades.

Authors:  Lulu Qian; Erik Winfree; Jehoshua Bruck
Journal:  Nature       Date:  2011-07-20       Impact factor: 49.962

Review 6.  Dynamic DNA nanotechnology using strand-displacement reactions.

Authors:  David Yu Zhang; Georg Seelig
Journal:  Nat Chem       Date:  2011-02       Impact factor: 24.427

7.  Abstractions for DNA circuit design.

Authors:  Matthew R Lakin; Simon Youssef; Luca Cardelli; Andrew Phillips
Journal:  J R Soc Interface       Date:  2011-07-20       Impact factor: 4.118
  7 in total
  34 in total

1.  Scaling down DNA circuits with competitive neural networks.

Authors:  Anthony J Genot; Teruo Fujii; Yannick Rondelez
Journal:  J R Soc Interface       Date:  2013-06-12       Impact factor: 4.118

2.  Computer-assisted design for scaling up systems based on DNA reaction networks.

Authors:  Nathanaël Aubert; Clément Mosca; Teruo Fujii; Masami Hagiya; Yannick Rondelez
Journal:  J R Soc Interface       Date:  2014-01-22       Impact factor: 4.118

3.  Modular verification of chemical reaction network encodings via serializability analysis.

Authors:  Matthew R Lakin; Darko Stefanovic; Andrew Phillips
Journal:  Theor Comput Sci       Date:  2016-06-13       Impact factor: 0.827

4.  Petri-net-based 2D design of DNA walker circuits.

Authors:  David Gilbert; Monika Heiner; Christian Rohr
Journal:  Nat Comput       Date:  2018-02-28       Impact factor: 1.690

Review 5.  Synthetic in vitro circuits.

Authors:  Adam J Hockenberry; Michael C Jewett
Journal:  Curr Opin Chem Biol       Date:  2012-06-05       Impact factor: 8.822

6.  A strand graph semantics for DNA-based computation.

Authors:  Rasmus L Petersen; Matthew R Lakin; Andrew Phillips
Journal:  Theor Comput Sci       Date:  2016-06-13       Impact factor: 0.827

7.  A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures.

Authors:  Stefan Badelt; Casey Grun; Karthik V Sarma; Brian Wolfe; Seung Woo Shin; Erik Winfree
Journal:  J R Soc Interface       Date:  2020-06-03       Impact factor: 4.118

8.  Individually addressable and dynamic DNA gates for multiplexed cell sorting.

Authors:  Shreyas N Dahotre; Yun Min Chang; Andreas Wieland; Samantha R Stammen; Gabriel A Kwong
Journal:  Proc Natl Acad Sci U S A       Date:  2018-04-09       Impact factor: 11.205

9.  Multi-threshold and multi-input DNA logic design style for profiling the microRNA biomarkers of real cancers.

Authors:  Mercedeh Sanjabi; Ali Jahanian
Journal:  IET Nanobiotechnol       Date:  2019-09       Impact factor: 1.847

10.  Analytical design of multi-threshold and high fan-in DNA-based logical sensors to profile the pattern of MS microRNAs.

Authors:  Mercedeh Sanjabi; Ali Jahanian
Journal:  Biomed Eng Lett       Date:  2021-05-11
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